Team:Groningen/Template/MODULE/project/MBD/bandage

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Bandage modeling
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Model-based bandage design
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Our main goal for this project is to design a bandage prototype for burn wounds. Burn wounds are usually infected with Staphylococcus aureus and Pseudomonas aeruginosa. The quorum molecules produced by these two pathogens should diffuse through the bandage and activate the production of Nisin, Aiia and DspB proteins. These three proteins should diffuse out of the bandage and act on the pathogens. <br><br>
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Our main goal for this project is to design a bandage prototype for burn wounds. Burn wounds are mainly infected with <i>S. aureus</i> and <i>P. aeruginosa</i>. The quorum molecules produced by these two pathogens should diffuse through the bandage and activate the production of Nisin, Aiia and DspB proteins. These three proteins should diffuse out of the bandage and act on the pathogens.
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<b>Bandage specifications</b><br><br>
 
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1. Top layer: Transparent polymethylpentene membrane permeable to gases, flexible and <br>
 
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2. Middle layer: Polyacrylamide hydrogel containing the chemically defined media and <br>
 
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3. Bottom layer: This layer acts as barrier for the Lactococcus lactis cells to be restrained hydrophobic. Lyophilized Lactococcus lactis cells. They are inactive since the gel is in dehydrated form. inside the bandage. Cellulose nitrate membrane of pore size 0.2 micrometers, permeable to protein, hydrophilic and flexible. <br><br>
 
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<b>Bandage model</b><br><br>
 
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To evaluate different bandage designs, we develop a multi-scale dynamic model of the bandage. The bandage is discretized into lattices where each lattice contains differential equations describing the growth of bacteria, production of nisin, production of Aiia, production of DspB and the detection of quorum molecules. Apart from the differential equations for the productions of the three IPM molecules we also consider the diffusion parameters. This makes the model more dynamic to study characteristics
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of our bandage. (Refer Figure 1 for all variables that are taken into account in the equations for each lattice). <br>
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</html>{{:Team:Groningen/Template/MODULE/newfigure|Figure 4|b/b5/Overviewmodel.modelling.png|
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Scheme for modeling the bandage
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Each state variable in each lattice is initialized according to the different bandage designs. Each lattice contains few bacteria which uses glucose as nutrient source and grows. Actively growing bacteria produce Nisin, Aiia and DspB only in response to the quorum molecules produced by both Staphylococcus aureus and Pseudomonas aeruginosa. In presence of quorum molecules in the lattice, the bacteria starts producing Nisin, Aiia and DspB. Nisin, Aiia and DspB produced in a lattice diffuses to nearby lattices until equilibrium is reached.
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To evaluate different bandage designs, we develop a multi-scale dynamic model of the bandage. The bandage is discretized into lattices where each lattice contains differential equations describing the growth of bacteria, production of nisin, production of Aiia, production of DspB and the detection of quorum molecules. Apart from the differential equations for the productions of the three IPM molecules we also consider the diffusion parameters. This makes the model more dynamic to study characteristics of our bandage.
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Each state variable in each lattice is initialized according to the different bandage designs. Each lattice contains few bacteria which uses glucose as nutrient source and grows. Actively growing bacteria produce Nisin, Aiia and DspB only in response to the quorum molecules produced by both <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>. In presence of quorum molecules in the lattice, the bacteria starts producing Nisin, Aiia and DspB. Nisin, Aiia and DspB produced in a lattice diffuses to nearby lattices until equilibrium is reached.
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Studying the diffusion rates of Nisin, Aiia and DspB is important to estimate the time taken to reach the threshold concentrations. The threshold concentration is the minimum concentration of the proteins that is required to breakdown biofilm, kill Staphylococcus aureus and quorum quench Pseudomonas aeruginosa population. The Diffusion constants for these three proteins were not available directly. They were calculated using number formulas which are listed below. Diiffusion rate inside the polyacrylamide gel is different from the diffusions in a solvent. The Diffusion rates for the proteins in polyacrylamide gel is calculated using the formula:
 
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Studying the diffusion rates of Nisin, Aiia and DspB is important to estimate the time taken to reach the threshold concentrations. The threshold concentration is the minimum concentration of the proteins that is required to breakdown biofilm, kill <i>S. aureus</i> and quorum quench <i>P. aeruginosa</i> population. The diffusion constants for these three proteins were not available directly.
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<a href="https://static.igem.org/mediawiki/2014/8/83/Rate_equations_for_diffusion_model.pdf">For more info on the rate equations look here.</a>
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Proin finibus nisi ut enim fermentum finibus ut egestas dolor. Vestibulum cursus eu dolor vehicula faucibus. Sed sed pharetra arcu. Pellentesque venenatis viverra justo a aliquet. Pellentesque venenatis viverra justo a aliquet. Praesent sit amet metus in ligula porttitor maximus. Pellentesque varius ligula lacus.
 
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Proin finibus nisi ut enim fermentum finibus ut egestas dolor. Vestibulum cursus eu dolor vehicula faucibus. Sed sed pharetra arcu. Pellentesque venenatis viverra justo a aliquet. Pellentesque venenatis viverra justo a aliquet. Praesent sit amet metus in ligula porttitor maximus. Pellentesque varius ligula lacus.
 
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</html>{{:Team:Groningen/Template/MODULE/newfigure|Figure 1|c/cc/Modelling_scheme_1.art.png|
 
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Proin finibus nisi ut enim fermentum finibus ut egestas dolor. Vestibulum cursus eu dolor vehicula faucibus. Sed sed pharetra arcu. Pellentesque venenatis viverra justo a aliquet. Pellentesque venenatis viverra justo a aliquet. Praesent sit amet metus in ligula porttitor maximus. Pellentesque varius ligula lacus.
 
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Latest revision as of 01:47, 18 October 2014

Model-based bandage design
 
Our main goal for this project is to design a bandage prototype for burn wounds. Burn wounds are mainly infected with S. aureus and P. aeruginosa. The quorum molecules produced by these two pathogens should diffuse through the bandage and activate the production of Nisin, Aiia and DspB proteins. These three proteins should diffuse out of the bandage and act on the pathogens.
 
Figure 4
 
Figure 4: Scheme for modeling the bandage
 
 
To evaluate different bandage designs, we develop a multi-scale dynamic model of the bandage. The bandage is discretized into lattices where each lattice contains differential equations describing the growth of bacteria, production of nisin, production of Aiia, production of DspB and the detection of quorum molecules. Apart from the differential equations for the productions of the three IPM molecules we also consider the diffusion parameters. This makes the model more dynamic to study characteristics of our bandage.
 
Each state variable in each lattice is initialized according to the different bandage designs. Each lattice contains few bacteria which uses glucose as nutrient source and grows. Actively growing bacteria produce Nisin, Aiia and DspB only in response to the quorum molecules produced by both Staphylococcus aureus and Pseudomonas aeruginosa. In presence of quorum molecules in the lattice, the bacteria starts producing Nisin, Aiia and DspB. Nisin, Aiia and DspB produced in a lattice diffuses to nearby lattices until equilibrium is reached.
 
Studying the diffusion rates of Nisin, Aiia and DspB is important to estimate the time taken to reach the threshold concentrations. The threshold concentration is the minimum concentration of the proteins that is required to breakdown biofilm, kill S. aureus and quorum quench P. aeruginosa population. The diffusion constants for these three proteins were not available directly. For more info on the rate equations look here.
 
 
 
 

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